From autodesk!smtpcc.autodesk.com!karynk@fernwood.mpk.ca.us Mon Feb 1 21:18:59 1993 Date: Mon, 01 Feb 93 17:31:57 PST From: karynk@smtpcc.autodesk.com (Karyn Kambur) To: hyperchem@autodesk.com Cc: karynk@autodesk.com Subject: HyperChem 2 minute survey Dear HyperChem User, I am conducting a survey to determine the following information; * societies and affiliations you belong to * HyperChem-specific applications that demonstrate how HyperChem helps you in your chemical research I would appreciate a few minutes of your time to answer these brief questions. Please return you answers and comments to me directly at "karynk@autodesk.com." Thank you for your support. 1. List the Societies and affilliations to which you belong; e.g. American Chemical Society, Protein Society. Please provide phone numbers for each if available. 2. What publications do you receive and read? 3. If you are in commercial or industry research, what application area are you currently working in: Medicinal/Pharmaceutical Organic Chemistry ProteinChemistry Biochemistry Inorganic 4. List the types of application areas HyperChem is used for. 5. Would you like to be a contributing author with your particular application? If yes, please let me know how I can best reach you. Once again thank you for your support. Karyn A. Kambur Autodesk, Inc. ________________________________________________________________________ From hyper!autodesk.com!burton@fernwood.mpk.ca.us Tue Feb 2 18:01:44 1993 From: hyper!burton@autodesk.com (Ian Burton) Subject: Deskjet 500C and 550C Workaround To: autodesk!hyperchem@fernwood.mpk.ca.us Date: Tue, 2 Feb 93 16:10:36 EST To All HyperChem Netters, For everyone who has been attempting to print CPK spheres from HyperChem to their DeskJet 500C or 550C printers, there is a simple workaround for V2.0 (Windows) to get around the banding problem. Printing in landscape mode instead of portrait will get rid of the banding problem. Changing to landscape mode can be done through the print manager through the Options menu and the Printer Setup option. Choosing the Setup button will open a dialog box that will allow you to set the landscape or portrait print modes. The quality of the spheres can be adjusted through the Options dialog box below the Deskjet Printer Setup dialog box (Yes, you will end up nested below about 5 layers of dialog boxes at this point!) Here, playing with the dithering, intensity and colour match will allow you to optimize the quality of the printout. Cheers, Ian Burton. -- Ian Burton Hypercube, Inc. Internet: burton@hyper.com #7-419 Phillip St. Telephone: (519) 725-4040 Waterloo, Ontario Facsimile: (519) 725-5193 Canada N2L 3X2 ________________________________________________________________________ From autodesk!uoft02.utoledo.edu!DSMITH@fernwood.mpk.ca.us Wed Feb 10 07:23:33 1993 Date: Tue, 09 Feb 1993 21:40:46 -0500 (EST) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: multiple cpu SGI machines To: hyperchem@autodesk.com Is Hyperchem going to run in parallel on the recently announced SGI machines? Doug Douglas A. Smith Assistant Professor of Chemistry The University of Toledo Toledo, OH 43606-3390 voice 419-537-2116 fax 419-537-4033 email dsmith@uoft02.utoledo.edu ________________________________________________________________________ From hyper!autodesk.com!burton@fernwood.mpk.ca.us Wed Feb 10 19:00:27 1993 From: hyper!burton@autodesk.com (Ian Burton) Subject: Re: multiple cpu SGI machines To: autodesk!hyperchem@fernwood.mpk.ca.us Date: Wed, 10 Feb 93 10:33:01 EST Cc: burton@autodesk.com (Ian Burton) > >Is Hyperchem going to run in parallel on the recently announced SGI machines? > >Doug > >Douglas A. Smith >Assistant Professor of Chemistry >The University of Toledo >Toledo, OH 43606-3390 > >voice 419-537-2116 >fax 419-537-4033 >email dsmith@uoft02.utoledo.edu > Dr. Smith, We already do. In response to your inquiry, the SGI Workstation release of HyperChem already does take advantage of multiple processors. In this release, there is a Communications... option in the Setup menu, which allows the user to specify the number of nodes which the computation will be distributed over, as well as specify whether the computation will be performed on the local or a remote host. After the number of nodes is specified, the kernel then is responsible for distributing these over multiple processors. If the number of nodes exceeds the number of processors, then the kernel may emulate multiple processes, but these will not be running in parallel. This should not change for the new SGI series of workstations. In release 2.0 of the SGI Workstation version of HyperChem Extended Huckel, CNDO, INDO, MINDO/3, MNDO, AM1, PM3, AMBER, BIO+ and OPLS methods all have the ability to run on parallel processors. Cheers. Ian. -- Ian Burton Hypercube, Inc. Internet: burton@hyper.com #7-419 Phillip St. Telephone: (519) 725-4040 Waterloo, Ontario Facsimile: (519) 725-5193 Canada N2L 3X2 ________________________________________________________________________ From autodesk!hyper!slee@hyper Thu Feb 11 15:17:44 1993 From: autodesk!hyper!slee@hyper.uucp (Thomas Slee) Subject: SCARECROW: 3rd party Molecular Dynamics Software. To: hyperloo@autodesk.uucp (hyperloo@autodesk.com) Date: Thu, 11 Feb 1993 11:29:23 -0500 I have sent the author of the following program information and samples of HIN and SNP files, and he is (as he states) including HyperChem in his list of formats. I believe the program is to be distributed for free, and some of its facilities are useful additions to HyperChem; specifically the calculation of "Connolly Surfaces" and the computation of radial distribution functions from liquid simulations. I will post again when I hear that the HyperChem implementation is complete. Tom ======================================================================== Forwarded message: >From uunet.ca!csc.fi!Leif.Laaksonen Thu Feb 11 11:06:36 1993 Date: Thu, 11 Feb 1993 02:52:32 -0500 Message-Id: <199302110752.AA07173@csc.fi> To: amber@cgl.ucsf.edu, charmm-bbs@emperor.harvard.edu, gromos@igc.ethz.ch, chemistry@osc.edu From: Leif.Laaksonen@csc.fi Subject: SCARECROW Computing Presents SCARECROW is a program for the analysis of MD trajectories. It has been published in the J. Mol. Graph. 10 (1992) 33. In fact the program is much more than just a MD analysis package. The package also contains: (1) The ICON8 extended Huckel program modified to eat 1000 atoms. There is an interface from SCARECROW to ICON8. The ICON8 program can generate the input to an electrostatic potential program (VSS). (2) The electrostatic potentiall program VSS. This is a c-code version of the old VSS program. The out put from VSS can be displayed with SCARECROW (3) A probe surface program to generate Connolly type of surfaces. (4) A program to generate orbitals or electron density data from orbitals generated with ICON8. SCARECROW is now able to read several different types of coordinate files like the CHARMM, INSIGHT, PDB and several other types of files. Trajectory analysis can be done for CHARMM, DISCOVER, YASP, MUMOD, GROMOS, and AMBER binary trajectories, and very soon also for HyperChem. Some of the goodies are only available for CHARMM users. New features in SCARECROW are the possibility to calculate radial distribution functions, power spectrum for main component analysis of time series and a possibility to calculate diffusion coefficients and much more. There is a very crude 2D display facility but the data can always be exported to your favourite plotting package. SCARECROW has a graphics interface and runs now only on Silicon Graphics Machines. On SGI machines it's also possible to run SCARECROW without graphics. I don't have any plans to port the stuff to other platforms, sorry. If you are interested to get more information about SCARECROW please feel free to get in touch. I have so far been distributing the program for free, if somebody makes money out of it I want to get my share. Cheers, -leif laaksonen --------------------------------------------------------- Leif.Laaksonen@csc.fi Center for Scientific Computing P.O. Box 405 FIN-02101 Espoo FINLAND Phone: 358 0 4572378 Telefax: 358 0 4572302 Voice Mail: 358 486257407 "In every job to be done there is an element of fun" Mary Poppins --------------------------------------------------------- -- Tom Slee Hypercube, Inc., #7-419 Phillip St., Waterloo, Ont. N2L 3X2 Internet: slee@hyper.com Tel. (519) 725-4040 ________________________________________________________________________ From autodesk!BIOLAN.UNI-KOELN.DE!PREINERT@fernwood.mpk.ca.us Sun Feb 14 20:08:56 1993 Date: Sat, 13 Feb 1993 14:38:58 +0100 (WET) From: PREINERT@BIOLAN.UNI-KOELN.DE (Peter Reinert) Subject: HyperChem on Indigo XS To: hyperchem@autodesk.com Hello, we have recently bought HyperChem to run it on a SGI Indigo XS. Now Autodesk in germany told us that we need an additional Z-buffer. This piece of hardware is three times the price of HyperChem and SGI says they will need about 6 weeks to deliver it. On the other hand out local SGI sales- man here in Cologne told me that all Indigos without hardware Z-buffer would simply emulate one, so he believes we could run HyperChem without the additional hardware. What shall we do? Could it be that our Indigo is not capable of emulating a Z-buffer because we have only 16 MB RAM at the moment (RAM upgrade already ordered)? Please help us, many thanks in advance! Peter Reinert Max-Planck-Institut fuer Zuechtungsforschung Koeln (germany) ________________________________________________________________________ From hyper!autodesk.com!slee@fernwood.mpk.ca.us Mon Feb 15 16:51:25 1993 From: hyper!slee@autodesk.com (Thomas Slee) Subject: Re: HyperChem on Indigo XS To: autodesk!PREINERT%BIOLAN.UNI-KOELN.DE@fernwood.mpk.ca.us (Peter Reinert) Date: Mon, 15 Feb 93 13:12:57 EST Cc: autodesk!hyperchem@fernwood.mpk.ca.us (HyperChem e-mail group) Dear Dr. Reinert, The situation with Z-buffers on SGI's is, as far as I understand, as follows. A Z-buffer is required for a great many 3D graphics apps. on an SGI: your problem and its solution will apply to any such software, not just HyperChem. The Z-buffer on all the SGI machines except the Indigo is implemented in hardware. On the base level Indigo it is emulated in software. HyperChem runs on either of these platforms, though somewhat slower on the Indigo because of the emulation. The XS Indigo has part of the function of the Z-buffer in its hardware, but not all. This means that there is no software emulation, and yet that there is no COMPLETE hardware Z-buffer. It falls between the two stools. The XS-24, on the other hand, has a Z-buffer in hardware. It is just your machine that doesn't have the Z buffer, and yet cannot emulate it in software. So, as I understand it, you will need to purchase whatever is needed to give you a Z buffer, in order to run HyperChem. Tom Slee > > Hello, > > we have recently bought HyperChem to run it on a SGI Indigo XS. > Now Autodesk in germany told us that we need an additional Z-buffer. This > piece of hardware is three times the price of HyperChem and SGI says they > will need about 6 weeks to deliver it. On the other hand out local SGI sales- > man here in Cologne told me that all Indigos without hardware Z-buffer would > simply emulate one, so he believes we could run HyperChem without the > additional hardware. What shall we do? Could it be that our Indigo is not > capable of emulating a Z-buffer because we have only 16 MB RAM at the moment > (RAM upgrade already ordered)? > > Please help us, > > many thanks in advance! > > > Peter Reinert > Max-Planck-Institut fuer Zuechtungsforschung Koeln (germany) > -- Tom Slee Hypercube, Inc., #7-419 Phillip St., Waterloo, Ont. N2L 3X2 Internet: slee@hyper.com Tel. (519) 725-4040 ________________________________________________________________________ From autodesk!autodesk.com!uucp@fernwood.mpk.ca.us Mon Feb 15 20:19:58 1993 Date: 15 Feb 1993 17:24:26 -0600 (CST) From: PELTERMW%PUCAL.BITNET@UICVM.UIC.EDU Subject: Driving Hyperchem with Visual Basic To: hyperchem@autodesk.com I just recieved a copy of Visual Basic 2.0 and tried the exercise in Lesson 15 (p213 of GETTING STARTED) and it doesn't work!!!! I'm having a problem with the line: text1.LINKEXECUTE "[do-single-point]" (with the last "t"!) ERROR MESSAGE ! DDE Method invoked with no channel open I followed the instruction as written. Any suggestions from anyone who has tried and succeeded with this lesson? Are there any corrections that should be added to the manual? Mike Pelter Purdue Calumet Hammond, IN 46323 peltermw@pucal.bitnet ________________________________________________________________________ From autodesk!kenyon.edu!batt@fernwood.mpk.ca.us Mon Feb 15 21:23:10 1993 Date: Mon, 15 Feb 1993 12:22:11 EST From: "R. BATT" To: HYPERCHEM@autodesk.com Subject: beta 2.5 With reference to the vibrational analysis feature in Beta 2.5, is there any way of making program think a couple of hydrogens in a molecule are really deuteriums? Russell Batt ________________________________________________________________________ From hyper!autodesk.com!slee@fernwood.mpk.ca.us Tue Feb 16 11:11:14 1993 From: hyper!slee@autodesk.com (Thomas Slee) Subject: Re: Driving Hyperchem with Visual Basic To: autodesk!hyperchem@fernwood.mpk.ca.us (HyperChem e-mail group) Date: Tue, 16 Feb 93 10:15:50 EST Mike Pelter writes: > > I just recieved a copy of Visual Basic 2.0 and tried the exercise in Lesson > 15 (p213 of GETTING STARTED) and it doesn't work!!!! I'm having a problem > with the line: > > text1.LINKEXECUTE "[do-single-point]" (with the last "t"!) > > ERROR MESSAGE > > ! DDE Method invoked with no channel open > > I followed the instruction as written. Any suggestions from anyone who has > tried and succeeded with this lesson? Are there any corrections that should > be added to the manual? > A two-part answer. First, the message is telling you that your command "Text1.LinkMode = COLD" did not manage to open a channel with HyperChem. The format for VB2 may be different from VB1 (which is what the example was done with: VB 2.0 was not released when HyperChem 2.0 shipped). However, even if you solve this, you will be in for a problem or two with the new version of Visual Basic, and this leads to the second part... This is a long story, still unfinished. Here is my current state of knowledge (personal opinions only, please note). When HyperChem 2.0 was released, the current version of Visual Basic was 1.0, and HyperChem 2.0 works just fine with VB 1.0. When Microsoft released VB 2.0 they redid their DDE stuff to use their new DDEML.DLL communications library. This is SUPPOSED to be 100% compatible with the older DDE: it is a management library (hence ML) that sits on top of DDE, as far as I understand it (and I am no Windows expert). But it isn't, and VB2 does not work with HyperChem 2.0. It will work just fine with the next release. Meanwhile, what can you do? Well, I hope to provide in a couple of weeks a VB 1.0 program to receive messages from your VB 2 program and pass them on to HyperChem (and vice versa). I can't guarantee it, but I have heard of somebody else doing this, and it does not sound too difficult. Tom -- Tom Slee Hypercube, Inc., #7-419 Phillip St., Waterloo, Ont. N2L 3X2 Internet: slee@hyper.com Tel. (519) 725-4040 ________________________________________________________________________ From autodesk!OSCA.osc.edu!osu982@fernwood.mpk.ca.us Wed Feb 17 12:12:59 1993 Date: Wed, 17 Feb 93 10:33:27 -0500 From: Lorraine Rellick Apparently-To: hyperchem@autodesk.com Dear hyperchem group, since it seems unlikely from the responses that I have already received that I can output the plots of charge density in a form that I can "use" (i.e., not metafile or bitmap - unless someone can point me in the direction of a really complete description of a metafile) - I was wondering if anyone can inform me of the algorithm to take the density matrix and generate the surface? - Any and all help will be greatly appreciated! - Lori Biochem dept OSU ________________________________________________________________________ From autodesk!uoft02.utoledo.edu!DSMITH@fernwood.mpk.ca.us Thu Feb 25 01:32:15 1993 Date: Thu, 25 Feb 1993 00:25:05 -0500 (EST) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: symposium: Modeling the Hydrogen Bond To: chemistry@osc.edu, mmodinfo@uoft02.utoledo.edu, hyperchem@autodesk.com Dear Fellow Computational Chemists: At the ACS National Meeting in Chicago, August 22-27, 1993 I will be chairing a symposium entitled "Modeling the Hydrogen Bond." I am starting in earnest the job of planning and preparing for that symposium, which is sponsored by the Computers in Chemistry division. Right now, it appears that we will have enough people for at least two days of talks and posters. There is still room for more, so... In order to assist in planning, I would ask that you, the readers of this mail exploder, help by letting me know if you are interested in speaking and/or presenting at this symposium. The more I know now, the more time and money I can ask for and the better the symposium will be. Please reply to me directly. If you have already spoken to me about presenting, you need not reply to this message Doug Douglas A. Smith Assistant Professor of Chemistry The University of Toledo Toledo, OH 43606-3390 voice 419-537-2116 fax 419-537-4033 email dsmith@uoft02.utoledo.edu